As per your suggestion, I am going to install Galaxy local and RNACHIPintegrator tool on my computer. Will be the display or interface of a local galaxy as same as Public galaxy server? I have another question regarding gene expression. How can I determine the up and down regulation of genes from Chip-seq data?

You will need to set up your local with the tools and data resources you want to use. There are resources for replicating Main, but this is usually wanted and implemented by an administrator creating a server as a service (local to some group or to be hosted publically). It takes considerable computing resources to fully replicate and support the work that can be done at http://usegalaxy.org and other Public Galaxy sites, even for a single server/user. Many choose to use Cloudman with AWS to build a server with the tools they need and compute resources on demand so that they don't need to invest in hosting it locally.

The analysis questions are big ones without a simple answer. There are many resources, publications, tool & tool manuals, help and message boards, etc focusing on these topics. Reviewing to get the bigger picture is important for any serious analysis.

That said, tutorials for Galaxy are available here: https://galaxyproject.org/learn/ You might find others on the web and/or relevant discussions here at Galaxy Biostars, although most are about the details - troubleshooting and the like.